Simulation of polymeric systems

计算机模拟已经成为研究复杂物理系统的一种流行方法。模拟是在计算机上使用一个简单的系统模型进行的人工实验，可以用来测试对实验的解释和分析理论中使用的近似。有许多不同类型的标准模拟技术，包括“分子动力学”和“蒙特卡罗”方法。除了这些方法，我还将测试和使用其他最近开发的更有效的方法，这些方法旨在正确地模拟流体中大分子的动力学行为。我使用计算机模拟方法来研究聚合物的物理行为。聚合物是任何长而灵活的分子，看起来像是由大量连接组成的链，称为单体。自然界中聚合物的一个重要例子是蛋白质分子，它是由氨基酸单体组成的。蛋白质经历了一个复杂的“折叠”过程，形成一个紧密的簇，从而能够完成其生物功能。我感兴趣的是阐明简单模型聚合物的一般物理行为，包括结构属性和动力学过程，以提供对折叠过程的洞察。我将回答以下问题。(I)聚合物与溶剂分子(溶剂是浸泡聚合物的流体，例如水)之间的相互作用力、聚合物分子本身的结构、聚合物在硬表面之间的限制以及沿聚合物的不同类型单体的排序如何影响聚合物的崩塌和冻结温度？(2)溶剂流动(“流体动力学”)如何影响聚合物在固定温度下的运动，以及聚合物在温度降低时坍塌和折叠的动力学路径？

Computer simulation has become a popular approach for the study of complex physical systems. A simulation is an artificial experiment conducted on a computer using a simple model of a system which can be used to test both the interpretation of an experiment and the approximations used in an analytical theory. There are many different kinds of standard simulation techniques, including "molecular dynamics'' and "Monte Carlo'' methods. In addition to these methods, I will test and use other, recently developed, considerably more efficient methods which are designed to model properly dynamical behaviour of large molecules in fluids. I use computer simulation methods to study the physical behaviour of polymers. A polymer is any long, flexible molecule that looks like a chain composed of a large number of links called monomers. An important example of a polymer in nature is a protein molecule, which is composed of amino acid monomers.  A protein undergoes a complicated "folding" process to form a compact cluster such that it can fulfill its biological function. I am interested in elucidating the generic physical behaviour of simple model polymers, including structural properties and dynamical processes, in order to provide insight into the folding process. I will address the following questions. (i) How do the interaction forces between the polymer and the solvent molecules (the solvent is the fluid in which the polymer is immersed, e.g., water), the structure of the polymer molecule itself, the confinement of the polymer between hard surfaces, and the sequencing of monomers of different types along the polymer affect the collapse and freezing temperatures of the polymer? (ii) How does solvent flow ("hydrodynamics") affect the motion of polymers at fixed temperature and the dynamical pathway as a polymer collapses and folds as the temperature is lowered?